Comparison between empirical protein force fields for the simulation of the adsorption behavior of structured LK peptides on functionalized surfaces

Biointerphases

Volumn 7, Issue 1-4, 2012, Pages 1-19

  Collier, Galen ^a   Vellore, Nadeem A ^a   Yancey, Jeremy A ^a   Stuart, Steven J ^b   Latour, Robert A ^a  

^a Clemson University   (United States)

^b CLEMSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADSORPTION; BIOINFORMATICS; MOLECULAR DYNAMICS; SURFACE PROPERTIES;

ADSORPTION BEHAVIOR; FUNCTIONALIZED MATERIALS; FUNCTIONALIZED SURFACES; PEPTIDE ADSORPTION; PEPTIDE CONFORMATION; PEPTIDE STRUCTURES; PROTEIN INTERACTION; REPLICA-EXCHANGE MOLECULAR DYNAMICS SIMULATIONS;

PEPTIDES;

PROTEIN;

ADSORPTION; ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; PROTEIN BINDING; SURFACE PROPERTY;

ADSORPTION; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEINS; SURFACE PROPERTIES;

EID: 84864108285     PISSN: 19348630     EISSN: 15594106     Source Type: Journal    
DOI: 10.1007/s13758-012-0024-z     Document Type: Article

References (51)

1. Leach AR (2001) Molecular modelling: Principles and applications, 2nd edn. Pearson Education Limited, Harlow
2. Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF (2004) J Comput Chem 25:1656-1676
3. van Gunsteren W, Billeter SR, Eising AA, Hunenberger P, Kruger P, Mark A, Scott WRP, Tironi I (1996) Biomolecular simulation: the GROMOS96 manual and user guide. Verlag der Fachvereine Hochschulverlag AG an der ETH Zurich and BIOMOS, Groningen
4. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher W E III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) J Phys Chem B 102:3586-3616
5. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) J Am Chem Soc 117:5179-5197
6. Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) J Am Chem Soc 118:11225-11236
7. DeGrado WF, Lear JD (1985) J Am Chem Soc 107:7684-7689
8. Phillips DC, York RL, Mermut O, McCrea KR, Ward RS, Somorjai GA (2007) J Phys Chem C 111:255-261
9. Apte JS, Collier G, Latour RA, Gamble LJ, Castner DG (2010) Langmuir 26:3423-3432
10. Weidner T, Samuel NT, McCrea K, Gamble LJ, Ward RS, Castner DG (2010) Biointerphases 5:9-16
11. Weidner T, Apte JS, Gamble LJ, Castner DG (2010) Langmuir 26:3433-3440
12. Weidner T, Breen NF, Li K, Drobny GP, Castner DG (2010) Proc Natl Acad Sci USA 107:13288-13293
13. Mackerell AD, Feig M, Brooks CL (2004) J Comput Chem 25:1400-1415
14. Vericat C, Vela ME, Benitez GA, Gago JAM, Torrelles X, Salvarezza RC (2006) J Phys Condens Mater 18:R867-R900
15. Grunze M (1993) Phys Scripta 1993:711-717
16. Latour RA, Rini CJ (2002) J Biomed Mater Res 60:564-577
17. Latour RA, Hench LL (2002) Biomaterials 23:4633-4648
18. Agashe M, Raut V, Stuart SJ, Latour RA (2005) Langmuir 21:1103-1117
19. Raut VP, Agashe MA, Stuart SJ, Latour RA (2005) Langmuir 21:1629-1639
20. Basalyga DM, Latour RA Jr (2003) J Biomed Mater Res A 64:120-130
21. Collier G, Vellore NA, Stuart SJ, Latour RA (2009) Biointerphases 4:57-64
22. Fears KP, Creager SE, Latour RA (2008) Langmuir 24:837-843
23. Tobias DJ, Mar W, Blasie JK, Klein ML (1996) Biophys J 71:2933-2941
24. Nordgren CE, Tobias DJ, Klein ML, Blasie JK (2002) Biophys J 83:2906-2917
25. Zhou J, Zheng J, Jiang S (2004) J Phys Chem B 108:17418-17424
26. Mar W, Klein ML (1994) Langmuir 10:188-196
27. Hautman J, Bareman JP, Mar W, Klein ML (1991) J Chem Soc Faraday Trans 87:2031-2037
28. Zheng J, Li L, Chen S, Jiang S (2004) Langmuir 20:8931-8938
29. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) J Comput Chem 4:187-217
30. Darden TA, York D, Pedersen LG (1993) J Chem Phys 98:10089-10092
31. Feller SE, Pastor RW, Rojnuckarin A, Bogusz S, Brooks BR (1996) J Phys Chem 100:17011-17020
32. Swope WC, Andersen HC, Berens PH, Wilson KR (1982) J Chem Phys 76:637-649
33. Evans DJ, Holian BL (1985) J Chem Phys 83:4069-4074
34. Ryckaert J, Ciccotti G, Berendsen HJC (1977) J Comput Phys 23:327-341
35. Yancey JA, Vellore NA, Collier G, Stuart SJ, Latour RA (2010) Biointerphases 5:85-95
36. Sugita Y, Okamoto Y (1999) Chem Phys Lett 314:141-151
37. Feig M, Karanicolas J, Brooks CL (2004) J Mol Graph Model 22:377-395
38. Frishman D, Argos P (1995) Proteins 23:566-579
39. Humphrey W, Dalke A, Schulten K (1996) J Mol Graph 14:33-38
40. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) J Comput Chem 25:1605-1612
41. Simmerling C, Strockbine B, Roitberg AE (2002) J Am Chem Soc 124:11258-11259
42. Kameda T, Takada S (2006) P Natl Acad Sci USA 103:17765-17770
43. Jas GS, Kuczera K (2004) Biophys J 87:3786-3798
44. Zhang J, Li W, Wang J, Qin M, Wang W (2008) Proteins 72:1038-1047
45. Zhang W, Wu C, Duan Y (2005) Convergence of replica exchange molecular dynamics. J Chem Phys 123:154105-1-154105.
46. Ruscio JZ, Fawzi NL, Head-Gordon T (2010) J Comput Chem 31:620-627
47. Grossfield A, Feller SE, Pitman MC (2007) Proteins 67:31-40
48. Faraldo-Gómez JD, Forrest LR, Baaden M, Bond PJ, Domene C, Patargias G, Cuthbertson J, Sansom MSP (2004) Proteins 57:783-791
49. Branden C, Tooze J (1999) Introduction to protein structure, 2nd edn. Garland Publishing, New York
50. Breen NF, Weidner T, Li K, Castner DG, Drobny GP (2009) J Am Chem Soc 131:14148-14149
51. Collier G (2011) PhD dissertation, Clemson University